2000 GT, 'Clunk' sound during initial acceleration & braking

Check your exhaust to see if it has broken a hanger. Or possibly a busted transmission mount.

+1 tranny or motor mount, that why you feel it when you take off because there stress through the drive train

+1 on the tranny mount,that would sound exactly the way you described it.

I would NOT drive it until it is fixed.What happens when the tranny mount goes bad is that the rubber part of it seperates then causes the rear of the tranny to hit the bottom of the car,mostly on acceleration and gear changes,Im not sure but with that much movement could possibly mess up the tranny shaft.

Also even if you did drive careful enough for it not to hit the bottom it is still goin to move,it may not hurt anything but I wouldnt risk it,I just had to get my tranny rebuilt,all the gears were good so I didnt have to replace those,just for beefed up synchros,shift forks,new seals and bearings...basic rebiuld cost me $420 only because I pulled the tranny myself,if I needed a total rebuild,gears,shafts ect....would have cost me $875,so if you did that kind of damage to it you cold be looking at that much since we have the same tranny's....another words I wouldnt risk it.Mounts are only around $100,not $100+$875 for tranny rebiuld.Just my opinion tho.Also whn I was a teen i bought a new 1992 Trans Am with a T5 tranny,I busted the tranny mount and continued to drive it(being young and dumb)and I did screw up the input shaft and the synchros because of it.

No one mentioned it, but you might want to check your dead space in your quarter panels for a beer bottle or something of that liking if you find that it's not your tranny mount. Just something else to consider.